Lack of a viable mechanism for producing high levels of complex and specified information.

The failure of the fossil record to provide support for Darwinian evolution.

The failure of molecular biology to provide evidence for a grand "tree of life."

Natural selection is an extremely inefficient method of spreading traits in populations unless a trait has an extremely high selection coefficient.

The problem that convergent evolution appears rampant -- at both the genetic and morphological levels, even though under Darwinian theory this is highly unlikely.

The failure of chemistry to explain the origin of the genetic code.

The failure of developmental biology to explain why vertebrate embryos diverge from the beginning of development.

The failure of neo-Darwinian evolution to explain the biogeographical distribution of many species.

A long history of inaccurate predictions inspired by neo-Darwinism regarding vestigial organs or so-called "junk" DNA.

Humans show many behavioral and cognitive traits and abilities that offer no apparent survival advantage (e.g. music, art, religion, ability to ponder the nature of the universe).

I started to work on the top 1000 problems with Intelligent Design Creationism but then I realized that it was a waste of time. There are only two essential problems with Intelligent Design Creationism: (1) There's no evidence for supernatural design in nature, and (2) There's no evidence for a supernatural designer.

They have a big problem with "sea monkeys". That is, that primates somehow got to South America from Africa across a (smaller) Atlantic Ocean in the Eocene. What they don't mention (or probably don't know about) is that rodents made the same trip at the same time, so there was obviously some means of dispersal possible for a small mammal that we don't yet know about.

But, apart from anything else, one problematical issue doesn't cancel out several thousand ones that are not. If science knew everything we'd all be out of a job.

The two essential problems with ID don't refute the first problem mentioned by Luskin, I think.

"Even leaving aside for now the problem of the actual origin of the very substantial complexity associated with the cellular level of organization, one cannot help wondering why the evolution of live didn’t stop at the stage of the simplest autotrophic prokaryotes, with 1,000 to 1,500 genes. Why insetad did evolution continue, to produce complex prokaryotes processing more than 10,000 genes, and more strikingly, eukaryotes, with their huge, elaboratedly regulated genomes: multiple tissue types; and even ability to develop mathematical theories of evolution?". Eugene Koonin. The Logic of Chance, 2012, 250.

Because there were (and still are) niches where complex prokaryotes could survive and outcompete simple autotrophs. Similarly, there were (and are) niches where complex multicellular organisms could survive and outcompete unicellular organisms.

There's no mystery there at all. Of course, it requires that there was some evolutionary path that would allow for development from simple autotrophs to more complex unicells to multicellular organisms. Obviously that's a path that Luskin (and, I suspect, you) don't think exists. But that's a different issue.

Why insetad did evolution continue, to produce complex prokaryotes processing more than 10,000 genes, and more strikingly, eukaryotes, with their huge, elaboratedly regulated genomes: multiple tissue types; and even ability to develop mathematical theories of evolution?". Eugene Koonin. The Logic of Chance, 2012, 250.

The answer to the question can be found on the next two pages in Koonin's book. Basically, it's the concept of non-adaptive genome evolution. Koonin argues that increases in complexity were actually neutral or maladaptive mutations that could not be overcome.

In other words, complex prokaryotes, and even more complex eukaryotes, are an accident of evolution.

the point is not that evolution didn't stopbut that it didn't stop to become as complex as it is now, including this eukaryote with a (mathematical) theory of evolution. Complexity is the issue here - and information for that matter

Besides, I was only referring to the first point of Luskin - no matter how 'sad' the rest of his list is.

The essential notion is this: There is no goal toward which life is evolving. All it can do, because of mutation, is evolve *from* where it is. The original simplest forms of life could not evolve into more simple life, because that wouldn't be life. It's like a bush growing against a wall - the only possible directions were equal complexity or greater complexity.

By far the dominant direction has been equal or nearly equal complexity. There are trillions and trillions more viruses, bacteria, and other very simple forms of life than there are of anything more complex. But yes, there have been occasional forays into greater complexity, that produced us along with other forms of life, since that was one of the possible directions for mutation to take.

Though this is awe-inspiring, when one looks at it in light of evolutionary theory it is not unexpected. It's simply what mutation does - it branches off in all possible directions.

Seems to me that given natural selection we would expect to see loads of convergent evolution, making Casey's #5 extra stupid (not terribly surprising, of course). And given what we know of the mechanisms for development, we might well expect to see the mechanisms for these convergences to be a mix of sometimes similar genetically and sometimes different -- just what we see. Yet more evidence that ID cannot make an accurate claim even after the fact.

Actually the IDs are just echoing-- somewhat confusingly-- what one reads in the scientific literature. Ernst Mayr famously predicted that the search for parallel genes and mutations underlying parallel changes would prove futile. Mayr's prediction follows from Fisher's rationalization of Darwin's pre-genetic concept of "natural selection" (which is the heart and soul of the Modern Synthesis) to the effect that smooth change happens at the phenotypic level because, at the genotypic level, there are infinitely many loci with variation affecting the trait, each one infinitesimal and additive. In this model, as in Darwin's original view, individual variations are like grains of sand-- each one is distinctive, for sure, but its uniqueness hardly matters because it is a tiny component of the whole sand-castle built by natural selection.

Thus, to Darwin and his 20th-century followers, the notion that similar phenotypic changes (i.e,. parallel or convergent changes) must reflect identical mutations is silly, like imagining that two similar sand-castles must have grains of sand that are identical. This is the logical basis of Mayr's theoretical prediction.

Mayr's prediction is famously wrong and is cited ad nauseam in the evo-devo literature. One also frequently finds statements revealing that the world's foremost experts on genotypic adaptation (e.g., Orr) understand that the emerging view of genetic adaptation is not the view advocated by 20th-century Darwinists.

So, to summarize, the issue that is problematic for Darwinism, neo-Darwinism, and modern neo-Darwinism (the Modern Synthesis) is the discovery of frequent parallel genotypic evolution. This is not a contradiction of evolution, nor of population genetics, nor of the principle of differential reproduction-- it is a contradiction of the infinitesimalist theory advocated by Darwin, Fisher, Mayr, etc.

Making a charitable interpretation of Complex Specified Information, we can equate it with "high enough fitness that in a set of random nucleotide sequences we would find fitness that high less than 10^(-150) of the time". Which organisms do achieve, in lots of ways and all the time. And which natural selection can get you to. Dembski's Law of Conservation of Complex Specified Information is of course (a) not proven, as you and Wesley Elsberry showed in 2003, and (b) formulated so as not assessing the right thing, as I showed in 2007. So the LCCSI fails to prevent natural selection from making fitness that nonrandomly high. So there is no problem in Number One.

Symbiotic cooperation produced eukaryotes. Combining recombination with reproduction (sex) allowed for large, more complicated genomes. Random mutations, random genetic drift, recombination, and non-random, fitness-guided natural selection (the major mechanisms of evolution) produced more complexity in at least some lineages. Development of collagen yielded multicelluar metazoans. Modification and duplication of Hox genes helped produce eumetazoans. Paedomorphosis and further Hox gene development helped produce bilaterians. You know the rest of the story (or maybe not).

At some point within bilaterians, another mechanism was added (sexual selection, very much nonrandom and, you might say, guided by intelligent beings). More than 500 million years after the first vertebrates (glorified worms with fins), one lineage developed stone tool technology, language, a very large and useful brain, an ability to transform the environment to its own ends, and eventually writing. At this point, education allowed cultural evolution to catch fire, leading to schools, universities, science, and eventually theories of evolution.

My comment was referring to Luskin's point 1. It is a straight invocation of William Dembski's Law of Conservation of Complex Specified Information. The stuff you quoted by Koonin is not responsive to that, or to the disproofs of the LCCSI. So irrelevant.

2. Are you arguing that random mutations produced (mathematical) theories of evolution?

The whole issue is not what random mutations alone do, but what natural selection can do once provided with the mutations as raw material. If you don't understand the natural selection part you aren't understanding modern evolutionary theory.

Jeffrey Shallit clearly hasn't read any molecular biology papers. If he had, he would have come across such terms as "functional specificity", "protein messages","complex motifs","intercell communication" and so on. The assertion that random mutations, which tend to scramble and mess up the information encoded in genes, are just capable of producing CSI is plain ridiculous. This is beyond the asinine.

The assertion that random mutations, which tend to scramble and mess up the information encoded in genes, are just capable of producing CSI is plain ridiculous. This is beyond the asinine.

Dembski's argument, which is the (only) basis for Luskin's point 1, is not an argument about what mutations do or do not do. It is an argument that natural selection cannot choose among different genotypes well enough to get the population out far enough on a fitness scale to find, for example, the best sequence out of 250 bases. In fact Dembski's argument is fallacious. It is that that we are discussing here.

3. The failure of molecular biology to provide evidence for a grand "tree of life."

Molecular biology provides tons of support for a tree of life, but it is not a perfectly exact tree of life (as there are such things as hybridization and horizontal gene transfer). Only by making a huge straw man by requiring an exact and perfect tree can Luskin say that evidence for it has not been provided. So Number Three is refuted.

Natural selection is an extremely inefficient method of spreading traits in populations unless a trait has an extremely high selection coefficient.

Where he gets this is a mystery. If the population size is, say, 1,000,000 (which is not that much for many organisms) then theoretical population genetics shows that selection coefficients will be effective if they are greater than ... wait for it ... 1 part in 4,000,000. Does that count as "extremely high"? Number 4 goes down the drain.

Joseph Felsenstein is of course right that, in populations of over 1 million, natural selection is highly efficient. But how many evolutionary biologists actually believe that populations of this magnitude are actually involved in speciation? On the contrary, most would state that major changes occur in small subsets of a population. For example, it is widely believed that our own lineage was created by a single founder member (the guy with the chromosome 2 fusion).

But how many evolutionary biologists actually believe that populations of this magnitude are actually involved in speciation? On the contrary, most would state that major changes occur in small subsets of a population. For example, it is widely believed that our own lineage was created by a single founder member (the guy with the chromosome 2 fusion).

The issue of whether or not there are bottlenecks in speciation is irrelevant to the matter, as there is no reason to believe that natural selection occurs only at such moments. Luskin's wrong point about natural selection is obviously based on someone's arguments but it is the only one of the 10 points that he does not give any link for. He says nothing about speciation or bottlenecks, he just declares change by natural selection to require unrealistically large selectiom coefficients.

I also agree with the preceding comment by Anonymous: whenever there is a mutation (or a chromosome rearrangement) that speakds through a population, we can say that everyone is descended from the one individual in which it occurred. Of course that does not mean that the population size was 1 at that time!

Instead of making errors like this, it would be more useful if you could unearth the source of the argument that Luskin is making -- where is he citing it from?

Oops, I erred. Luskin does have one other of his points that is not referenced by any link: the utterly silly #10. (So I gave him too much credit). Luskin himself also, in the comments section of ENV, diverts discussion of #1 away from Dembski's argument -- but it is clear from his terminology that Dembski's LCCSI is the basis of what he says.

The point I make is that significant phenotypic evolution is believed to happen not in the big populations that you like - i.e. in the model of phyletic gradualism - but rather in short bursts involving a bottleneck or some sort of reproductive isolation and/or migration event. In their immediate aftermath, genetic drift is a much bigger factor than selection. At least in the case of human origins, we are dealing with very small populations with lots of inbreeding which also reduces the efficacy of selection.

Joe Felsenstein is, of course, right to attack Luskin's assertion that natural selection is inefficient per se. I agree with the maestro entirely. There does not have to be an extremely large fitness gain associated with a trait for positive selection to promote it.....BUT...JF is not giving us all the full context:

1. If the interbreeding population size is small, and gene inflow is low, selection is less effective.

2. If the mutation rate of the allele responsible for the trait is very low, this lowers the probabiity of fixation.

3. If the trait is polygenic, and involves complex epistatic interactions, selection's power may be lessened.

4. If the genes associated with the trait are physically linked to harmful loci, this can potentially neutralize any fitness gain.

5. If there is a pleiotropic side effect associated with the trait, this can also compromise the efficiency of selection.

So, I suspect Luskin's words do contain an ounce of credibility when you factor in *realistic conditions*.

1. False. Alleles can spread faster in smaller populations.2. False. If the mutation rate is low, then fixation is a natural outcome.3. If the trait is not polygenic?4. If the genes associated with the trait are not physically linked to harmful loci?5. If there is no pleiotropic side effect, of if the pleiotropic side effect is not harmful?

I suspect that we can find all kinds of scenarios. From problematic to highly evolvable. So what? How does either your ability to list negative scenarios, or mine to list positive ones, affect whether evolution works all by itself or not?

I'd like to know how JF thinks the chromosomal fusion (of 2a and 2b) could have spread through the population when it effectively serves as a reproductive barrier. The guy with the fused chromosomes would likely not have been able to mate with anyone other than those with a similar condition. It is one reason why humans and chimps cannot interbreed successfully (not that I would want them to).

Larry says “There's no evidence for supernatural design in nature.” - While there are lots of round and cylindrical living things, there are almost no square plants or animals. Why isn't there any animal that has a skeleton made out of metal? And while there are so many ways for living things to move about, why do almost none of them have wheels? Humans make lots of square things, use metal frames in the things they build, and use wheels on lots of moving things. But these features don't offer good solutions for the things with which most living things must deal. Wheels are useless for going through the jungle, climbing trees, flying or burrowing. In engineering language, all living things show a high degree of design sophistication (evidence for a Creator). For example, the skeletons of all mammals have a ratio of 30% shock-absorbing collagen to 70% calcium phosphate for strength. This ratio provides the very best balance for holding up a mammal's weight during locomotion. Engineers also know that in order to get the best flow of a liquid - such as blood - a pipe's cubed radius must equal the sum of the cubed radii of each of its branches. This is exactly the kind of ‘evidence’ found in all living and fossilized creatures, from sponges to humans (evidence for a Creator)! The impressive engineering found in all living things - and even in the oldest fossils - offers elegant testimony to a Creator. What is a FACT is that we do not find in nature shapes and functions that are random, unsophisticated, and simple vs. complex. What is in FACT the case is that all life on earth and all the processes of the laws of cosmological physics show obvious guided, designed, sophisticated, and ordered complexity, so much so that it takes countless fields and sub-fields of science to cover them. And, all this complex evidence shows that it takes a lot more work (or atheistic bias) to believe in random evolutionary chance than it does to believe in a Creator.

Why is it it a FACT that the creator forget to put gills on whales, seals, turtles, and all other amniotes that live partly or wholly in the water? Why is it a FACT that whenever creationists argue against "random evolutionary chance" they forget about natural selection? Why is it a FACT that they forget that fractal branching networks produce apparent complexity with very simple rules and therefore do not necessitate their favorite mythical sky daddy? Why is it a FACT that creationists forget that natural processes can produce ordered complexity?

Once again, Mr. Denny demonstrates his abysmal ignorance of evolution. Natural selection is not a random process. However many times Mr. Denny is told that, he persists in ascribing only randomness to evolution. Either he has a reading comprehension problem or he is a liar.

Regarding Neil deGrasse Tyson's 'bad design' arguments, they've been trotted out throughout the ages by critics who posit that a 'true god' would have designed a Utopian realm. Not so. Theme Park Earth follows an obvious patten of a competitive arena, which is just what the doctor ordered.

But in reality, evolution is true (accolades to Coyne), but the evidence of totally uncaused causality, save by opportunistic occurrences is in serious doubt. In short, complexities and systems offering no immediate survival or reproductive advantages, whether large or small populations, would not be selected upon. Nor would they occur in most instances.

Evolution as observed is basically embryonic reproduction, with the added feature of adaptive selectable modifications as needed. But novelty to deviated radically from a genera would be rare, if at all occurring.

I posit design intervention at select times by multiple designers via genetic modification. MDT as a tentative theory appears to have some viability. And while Richard Hoppe is definitely not a 'creationist', nor am I, he excels at rational thought.http://pandasthumb.org/archives/2004/09/introduction-to.html

the skeletons of all mammals have a ratio of 30% shock-absorbing collagen to 70% calcium phosphate for strength. This ratio provides the very best balance for holding up a mammal's weight during locomotion.

Denny, you ought to be able to spot the logical fallacy in this one yourself with just a moment's thought: The bony/collagen skeleton precedes all forms of mammals, and thus of mammalian locomotion. So you have your design "effect" preceding by millions of years its supposed "cause."

And by the way, which form(s) of locomotion are you referring to? Bipedal, quadrupedal, swimming, flight...? Mammals use all of these forms of locomotion.

Why do dolphins and whales need the same shock absorbing properties in a skeleton that land-dwelling mammals do? And as long as we're discussing skeletons, what is the design reason for the vestigial internal rear leg and foot bones in whale skeletons? Or is it just possibly that as the fossil and genetic evidence shows, they evolved from land mammals that had back legs and feet, and evolution just had to cope as best it could when the offspring of those land mammals began to spend all their time in the water?

Your flavor of ID is different than the one offered by Luskin and Denny does differ in how awesome the designer is. But we were debating Luskin and Denny's version (the Christian God) who seems, by description, to not be one to make such bad design.

Regarding yours, I ask again, who designed the designer? The introduction of a designer of any type just delays this same problem by one step. The religious invoke a super-being beyond the laws of space and time. How did your designer come to be?

"Who designed the designer" is a question that make an assumption, to wit that my 'design inference' premise is based on a preconceived notion, ergo a religious view. Both you, Dawkins and David Hume are asking an unanswerable question.

I assume you hold to the Big Bang theory, right? Then answer me this, a question of the same validity: What set it off? Effects are often observed w/o a delineation of causality.

ID does NOT postulate 'a designer', and in particular, a supreme god. Just because some of its adherents hold religious views that do, the 'Supreme God' premise is NOT a premise within ID, a further reason to discredit your (and Hume's) question.

Design, where inferred, is just that, i.e. evidence that more than unguided natural causation can account for specific components within phylogenetic progressions (complexity, co-dependent systems, and novelty). ID makes no attempt to explain causalities from an identity standpoint.

I assume you hold to the Big Bang theory, right? Then answer me this, a question of the same validity: What set it off?

The most likely hypothesis is that a transient discontinuity in the quantum vacuum resulted in the creation of the matter in the universe. Because of CP violation, more particles then anti-particles were created so that the annihilation of particle/anti-particle pairs did not result in a return to the quantum vacuum, i.e. a residue of particles remained.

Incompleteness is also an opportunity for younger scientists to shine. If every theory was complete and explained everything, the job could be turned over to the applied scientists and engineers and the biology, physics, astronomy, chemistry, etc. departments in universities could be shut down. Fortunately, that is highly unlikely.

There are gaps even in physics. For instance, there is no theory of quantum gravity but that doesn't mean that relativity and quantum mechanics are going to be abandoned.

It has been a long time since I studied any chemistry, but is not calcium classed as a metal? So it is not used in its metal form in skeletons, but that would not work very well, considering the highly reactive nature of metallic calcium. Why should life forms go to any other metal for structural support, when calcium is so abundant and combines so well with other chemical elements?

Assuming the criticisms to be sincere, it is useful to try to see what errors in thinking underly them. #1,4&5 seem to be based on an inability to grasp deep time.

#10 appears to reflect a standard confusion with evolutionary theory as requiring everything be adaptive, one that is shared by researchers trying to show, for instance, that "religion" is indeed a biologically based adaptive function of the brain. I don't know how you can authoritatively refute this when other authorities agree.

#6 is not part of evolutionary science. But it's hard to see how that can't be very easily construed as a cop out. Aside from the difficulty of grasping the roles of deep time and the true size and complexity of the Earth, the facts and theories are not as well developed and are much more convincing to those who already accept a naturalist approach.

#2,3,7&8 seem to me to reflect a fairly common falsificationist approach. Logical or mathematical proof is acceptable but other theories' credibility rests solely upon falsification. Thus the existence of any puzzles remaining serve in their view to falsify the theory. Again, it seems like it would be very difficult to refute this approach since so many scientists vociferously adhere to a falsificationist position. The comment above, that the many successes of theories still counts, is not a principle agreed to by falsificationists. Perhaps there's some distinction somewhere between naive and true falsificationism but I've not found it anywhere yet myself.

#9 is curious. Lateral gene transfer make a puzzle for the "tree of Life." The "sea monkeys" are a puzzle in biogeography. There are always gaps in the fossil record (at least until new fossils are found," and always will be, due to imperfections. Fixed notions about the due rapidity of divergence in embryological development will find puzzles. And all these puzzles will seem to refute evolutionary science. But whatever is the problem with vestigial organisms and "junk" DNA? Is it the old idea that everything is adaptive?

I'd say one of the big problems with Darwinism is that many people, both for and against it, insist that it has a fixed, absolute position in science that it doesn't have.

Oh, nuts. The world is burning, species are being destroyed in a man-made extinction event and I'm supposed to care about species that died off ages ago (literally). There are bigger fish to keep from frying.

I said what I said. The Darwin Wars are interminable with so many lies told on all sides that, as a political-ideological phenomenon, they can't be settled. They are mostly not worth the trouble. Certainly not as compared to preserving what evolution has produced, whether designed or not.

This isn't evolutionary biology, it's ideological babble. If atheists didn't endlessly assert that it was the nail in the coffin of God it would have probably never have developed into the disaster it's become for science.

1. Natural selection is a conserving force in Nature. It tends to reduce variation rather than promote it. It is anti-evolutionary.

2. As Luskin says, natural selection acting on random mutations does not adequately explain the origination of the important protein motifs that are at the heart of cellular activities. At most, natural selection can tweak existing functionality.

3. An even bigger problem is that genomes don't seem to contain any morphological information. Neo-Darwinism believes that all phenotypic change occurs in DNA but the diversity of form in the living world appears not to be correlated to chromomsomal material.

So, as prosecutor, judge and jury, I therefore pass sentence and condemn Darwinism to intellectual oblivion - and with no hope of parole or reprieve.

"Natural selection is a conserving force in Nature. It tends to reduce variation rather thaan promote it."

That might be true in an unchanging environment where all available niches are occupied by near-maximally adapted organisms. Such conditions do not apply to Earth; certainly not on evolutionary timescales.

1. Natural selection is a conserving force in Nature. It tends to reduce variation rather than promote it. It is anti-evolutionary.

Both Natural Selection and Drift tend to reduce variation rather than promote it. But you should, by now in your tireless Internet career, have come across these other evolutionary forces Mutation and Recombination. The variational and fixational forces TOGETHER form evolution. There isn't an 'evolutionary bit' and an 'anti-evolutionary bit'.

When you introduce variation (by mutation or producing new combinations), Selection/Drift tends to eliminate it again. This does NOT mean that a population must therefore remain static - far from it. Can you really not see why? You appear to say that selection must always eliminate the most recent variant. How does it know which one that is?

2. As Luskin says, natural selection acting on random mutations does not adequately explain the origination of the important protein motifs [...]

There are gaps in our knowledge? The hell you say! The jig's up, evolution is dead, long live the detailed explanation of the origin of these 'protein motifs' provided by good old ID. Feel free to fill us in on what that is.

3. An even bigger problem is that genomes don't seem to contain any morphological information [...]

Development is not genetically controlled? Haha! Something non-heritable is at work, you think? A protein, perhaps? Produced by ... oh, never mind.

I have repeatedly raised the issue of protein motifs because, if the Darwinists actually provided a testable and plausible explanation for their origination, their ideology would become greatly more convincing and appealing to me. But all they do is just invoke natural selection like it were some magic wand.

There is no "body plan" contained in the genome. None of the biological structures and systems in your own body are represented somehow in DNA. Sure, protein production is absolutely necessary for morphogenesis to occur, but it doesn't explain why cells coalesce to form particular shapes of biological function.

I have repeatedly raised the issue of protein motifs because, if the Darwinists actually provided a testable and plausible explanation for their origination, their ideology would become greatly more convincing and appealing to me.

I seriously doubt that. But the fundamental requirement for making a protein 'motif' is the same as that for making any peptide chain - peptidyl transferase activity. Since you can't make protein catalysts without peptidyl transferase, early peptidyl transferase must have been a non-protein activity. It still is - things would get pretty messy if a protein tried to make protein.

What's the shortest possible functional peptide chain?

You can make some of the simpler motifs with just a handful of residues, or even a repeated unit such as polyglycine. You can combine different motifs in modular fashion to form higher-order structures.

If every motif were dozens of residues in length, unrelated to all others and destroyed by the smallest substitution then yeah, maybe there would be an evolutionary puzzle. But that's not how it is.

I would like to reply to the argument from incredulity about "random mutations producing a mathematical theory of evolution".

No one knows exactly how our minds work, but I have some evidence that my mind works by ... random mutation (of ideas). That is, trial and error combinations, sorted through by the 100 billion synapses of my neurons, which are not under my conscious control.

My first evidence of this is that in 35 years of working as a design/development engineer for General Electric, every "new" design I saw was a small incremental improvement of previous designs, and left room for further incremental improvements. That is to say, "designs" don't appear by some supernatural process; they evolve. (Often by stealing ideas from somewhere else - horizontal gene transfer. Our cleverest idea for a way to design a new type of turbine vane shroud came from someone's recollection of a lathe chuck.)

My favorite example of this comes from Cooper Industries (now Rolls Royce Energy Services) in Mount Vernon, Ohio. In the 1950's they were supplying steam engines to farmers, to power threshing equipment. The steam engines were transported to crop fields on wagons, along with wagons full of coal, to fuel them. The wagons were pulled by teams of 12 to 14 draft horses - until someone at Cooper got the idea of using a bevel-gear wheel (as used in water mills) to connect the output shaft of the steam engine to the rear axle of its wagon. There is a large oil painting of the result in the plant's main building. Instead of 12-14 draft horses, the wagon has ... two draft horses. They were used to steer the vehicle.

That is how radical inventions like the farm tractor were developed, one trail-and-error step at a time. As far as I know, the supernatural design process which the ID people seem to believe in does not exist.

The next evidence I can cite came from my own investigation of Fermat's Prime Theorem, which I read about in Simon Singh's "Fermat's Enigma" - the theorem that every prime number which is of the form 4N+1 is the sum of two squares (5 = 1 + 4, 13 = 4 + 9, etc.) That seemed an interesting, non-obvious result, and I decided as an intellectual challenge to try to prove it. I spent over a year on it, often working six or eight hours a day (in my retirement). I wrote large Excel spreadsheets which did various calculations with 4N+1 numbers, from N=1 to several thousand, and looked for patterns. Some of my best thinking seemed to be done on long walks, without even a scratch pad and pencil. That seemed to free my mind for ranging over and combining ideas, rather than focusing on one thing. Finally, I came up with a combination of ideas which, after some iterations to remove errors, satisfied me as a rather clunky but sufficient proof.

I came away from that process convinced that was accomplished by random neuronal trials. I would invite readers (if any) to tackle the same or a similar mathematical problem and see if they do not observe the same thing.

This also answers the incredulity some claim to feel over the fact that evolution created a being capable of understanding the universe as well as we do, via our mathematical models. The answer of course is that if random trial and error and guiding criteria for success (natural selection) did not work in this universe, than neither would our mathematical models (which we would not exist to create). There is complete consistency, as I see it, between our success (such as it is) and evolution's (such as it is).

did you actually observe those random neuronal trials? You make it sound like Edelman's neural darwinism, an idea that was criticized by the late F. Crick.

There a few attempts to model replication (and selection) in the brain, but there's a more fundamental problem here, I think. Though he wasn't the first one, Haldane's formulation is one of the clearest, as far as I know:"It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms." Haldane, J.B.S., Possible Worlds: And Other Essays 1927,.209

Right. As you can see below, I posted a correction two minutes after my original comment, but unfortunately I can not edit the original comment on this site - and my mechanically-processed brain is very prone to typos of that sort. I blame evolution.

Anonymous said, “Why is it a FACT that the creator forget to put gills on whales, seals, turtles, and all other amniotes that live partly or wholly in the water? Why is it a FACT that whenever creationists argue against "random evolutionary chance" they forget about natural selection?” – The Creator didn’t forget anything. Your question is bogus. Whales, seals, and turtles are mammals. Also, my use of the word chance is intended to be a synonym for all the evolutionary expressions that attempt to explain how something came from nothing, how life emerged from non-life, and how slow moving mutations sped up once in a while. All are attempts to refute the obvious evidence for something that is extra-material and more demonstrative of a Creator than a non-created process.

SLC said, “Either he has a reading comprehension problem or he is a liar.” – What an interesting word (“liar”) for a materialist to use. It implies something non-material.

steve oberski, said “Keep up the cut and pasting.” – No cutting and pasting by me, just you cutting and pasting web links I’ve never seen. It’s only common sense to think that if random chance, or natural selection, as you may chose to call it, any unguided non-intelligent process produced everything, there would be a lot more weird species variation.

Anonymous said,” One guy's examples... http://www.youtube.com/watch?v=oEl9kVl6KPc.” - I have referred to Neil deGrasse Tyson many times. I have drawn from the link you note. He’s very smart and very entertaining. For quote mining fans, here’s one by Tyson, “The more I learn about the universe, the less convinced I am that there's any sort of benevolent force that has anything to do with it, at all.” If a proper definition of science is ‘knowledge of the natural world,’ then his comment about a “benevolent force” is scientifically irrelevant, and he is curiously mixing the natural with the supernatural, of which he is clearly no expert. He is also very enthusiastic about evolution. Here’s more Tyson quote mining, “The universe is expanding on a one-way trip to oblivion!”? Tyson’s use of the word “oblivion” reveals both a purely realistic scientific view, and a qualitative view that seems counter the notion of materialism. This is a cosmological scientific viewpoint, which is consistent with every other notable evolutionary icon I know of. In the video/link you provide, Tyson does not seem so excited about “oblivion”.

Shit Denny, how many times do you have to read that natural selection is not "random chance"? Using the words "random chance" to describe anything and everything not involving your believed and beloved myths (your god(s)) might be all right for you, but it makes communication with you impossible because the words have a meaning that is not the one you pretend and presume to use. They do not convey the ideas of atheists, of materialists, of evolutionary scientists, of cosmologists, of physicalists, of naturalists, of objectivists, long et cetera-ists, at all. So, they come and look like mere attempts at making any natural explanations to the universe and everything into straw-men. Thus also reducing your capacity to understand any explanations given. But i suspect you don't give a damn about those explanations. AFter all, you quickly put everybody into a single category instead of asking or wondering if, say, SLC, or Neil deGrasse Tyson are materialists. I suspect you also divide the whole of philosophical stands into materialists and theists, ignoring an incredibly rich number of philosophical stand points. Many of them not mutually exclusive.

I have a question for Mr. Denny. Ken Miller and Francis Collins accept methodological naturalism but profess to be philosophical theists. Are they materialists?

As for the word liar, I fail to see why that has anything to do with materialism. It merely is a description of one who tells things that are not truthful. For example, one who persists in referring to evolution as a random process, even after being corrected multiple times, is one who tells things that are not truthful.

By the way, relative to Mr. oberski's comment about cutting and pasting, it is considered a violation of internet protocol to copy and paste material from another site without providing a link to that site.

Re: "if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true."

I see that as partly an argument from incredulity - the inability to see how mechanical means can sort through alternatives to find some which fit some criteria, which is not a problem to me since I am familiar with computers and the Monte Carlo method - and partly as a non sequitur: supposing mental processes were formed in some other way - by magic, for example - how would that give any reason to suppose beliefs are true? Can't beliefs formed by magic be false?

The best way to decide whether beliefs, however formed, are true or false, it seems to me, is to check whether they work, via the scientific method. Mechanical methods, as done in computers using atoms, have passed such tests. I have designed turbine components using such methods, and those turbines are operating successfully as I type.

Professor Haldane would have been well-advised not to assume any of his beliefs were true, but to test them and find out; or where untestable (in his time) to hold them with some humility. (No doubt I fail in that as often as he did.)

I think the problem Haldane is trying to make is reductionism. 'All the arrows of explanation are pointing downwards', but still it is difficult to get upwards again, from the particles and forces back to the mind: reduction is easier than reconstruction (Anderson, more is different, 1972). That's the point I think. It's easier to test your beliefs about turbines, or computers for that matter, than ideas about the mind.

Yet we know, thanks to Turing, that all the complex instructions which allow our computers to send information back and forth over the internet (and allow Siri to answer the question, "Is it raining?") can be reduced to a bunch of nested NAND circuits. So in fact the evidence that reductionism can work, from that one example, is quite powerful, it seems to me. (Haldane of course did not know this; I'm not sure about your Anderson - computers were not as amazing in 1972.) Bear in mind that we have not yet been able to build a super computer with the equivalent of 100 billion synapses.

In any case, the logic of Haldane's case still escapes me. One of his premises seems to be that mechanical, reductionist processes are capable of, or even prone to, error. I would agree with that. But the world is full of false beliefs (possibly including all of us, at one time or another) - so no inconsistency with observation there. That's why we need the scientific method, to keep us honest.

"So in fact the evidence that reductionism can work". Indeed, it works that way. Right. Thanks to Turing. I think that's the point Anderson (and other 'anti-reductionists' like e.g. R. Laughlin in physics, or Goldenfeld and Woese (2011) in biology) are trying to make: how do you get up from these circuits all the way to Turing. Or, how do you get (back again) from molecule to man? That's not a moot question as the people I mentioned, have shown.

Anderson doesn't mention computers. He's talking solid state and body physics as an example, arguing that 'psychology is not applied biology, nor is biology applied chemistry'.

I was not saying that reductionism doesn't work, or that it's not powerful.

Over at ENV's list of Top 10 problems for evolution, I submitted this rebutall to Casey's #9 (Junk DNA). I don't think the hyperlinks will work here, but here it is for your perusal.

As for Casey’s #9, “Junk DNA”: the ID movement has a long history of misrepresenting genetics, both cutting edge research and the history of science, and that is the case with Luskin’s and Jonathan Well’s gross misrepresentations about molecular biology, junk DNA, and the history thereof. Wells and Luskin have promoted the absurd falsehood that molecular biologists believed non-coding DNA was non-functional “junk.” Utterly false. Molecular biologists believed (and still believe) that non-functional DNA is “junk”, not non-coding. The mythology that molecular biologists believed ‘non-coding = non-functional’ is a figment of the creationist imagination, aggressively promoted.

Every molecular biology grad student since the 1970’s has known—and had to know—that regulatory elements are in non-coding regions. Jacques Monod was awarded the Nobel Prize in 1965 for showing that regulatory elements are in non-coding DNA, so the Nobel Committee had to know. Every mol. bio. grad student knows that he has to control induction of genes he clones in, and control of induction means binding (or non-binding) to regulatory elements in non-coding regions.

For a lawyer like Luskin to accuse molecular biologists of saying that ‘non-coding = non-functional’ is like lecturing the police that their job requires catching criminals. It is like a sports fan telling quarterbacks that goals are made by getting the football into the end zone. It is fantastically insulting. The scientific community will never forgive ID proponents for inventing the ‘non-coding = non-functional’ myth.

Secondly, scientists did not predict that most DNA would be junk (most of it is still junk, today, AFAWK) because of “neo-Darwinism.” No sir: scientists believe bacteria are a product of evolution, and everyone knew they have no junk DNA. No scientist would say, as Luskin and Jonathan Wells caricature, “Bacteria are the products of ‘blind chance’ and ‘accidents’, so they must have lots of junk DNA.” Any scientist would choke on that, because they know bacteria don’t have junk DNA.

As has been repeated endlessly, in the 1960’s there were opposing schools of thought who added to evolutionary theory very different assumptions about the strength of selection and the cost/benefit ratio of a high mutation rate. The “adaptationists” thought selection was strong, and the costs of a high mutation rate were low, the benefits high. The “neutralists” thought selection was weak, and the benefits of natural selection not strong enough to outweigh the huge number of possible neutral mutations. “Adaptationists” would expect little or no junk DNA, “neutralists” would allow for junk DNA (not require it). “Junk DNA” does not follow from ID’s gross cartoon of “neo-Darwinism,” but rather from evolutionary theory plus observations that genes and regulatory elements together make up a small part of the genome, plus assumptions about cost/benefit ratios.

Fast forward to the present: the neutralists were right, at least about complex animals and plants; most nucleotides in the human genome are not biochemically constrained by any functional constraint. Mostly still junk. For bacteria, which have no junk DNA, the adaptationists were right. Some amoeba and dinoflagellates have more DNA than humans; some plants have 50 times more DNA than humans. This is because the cost/benefit ratio is different for bacteria vs. for complex organisms.

Thirdly, the human genome is mostly still junk. Most nucleotides in the human genome are still not biochemically constrained as to sequence, and no ID proponent has ever offered any evidence to contradict this. Jonathan Wells and Luskin have used innuendo and vague terminology to state, or to imply, that most DNA in the human genome is functional. This is false, AFAWK.

Continuing with my post to Luskin's "junk DNA" claim in the list of Top 10 problems with evolution [part 2]:

These innuenodoes and false statements from ID proponents fall into three categories.

Category #1: I’ll call “vaguediction.” This includes the use of weasel words to give a false impression of how much DNA is known to be functional—for instance, “much.”Jonathan Wells: “The arguments by Dawkins, [Ken] Miller, Shermer, [Sean] Collins, [etc.] rest on the premise that most non-coding DNA is junk, without any significant biological function. [But] Much of the DNA they claim to be "junk" actually performs important functions in living cells.” [Well, The Myth of Junk DNA, p. 27. Note the first part of this sentence dishonestly portrays molecular biologists as believing ‘non-coding DNA = non-functional DNA.’]

William Dembski: “If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function.”—[First Things, 86, 21-27]

What does “much” mean in the sentences above (note Mr. Luskin has made “much” statements many times)? “Much” is deliberately vague in order to be non-falsifiable.

By “much” do they mean ten million nucleotides? Ten million might impress non-scientists, but it’s 0.3% of the genome. Does it mean 90% of the nucleotides in the genome? If that’s what they mean, it’s a factually false claim. This vague terminology--“much”-- impresses non-scientists, but scientists find it infuriating. Does “much” refer to an absolute count of nucleotides (in millions) or a relative fraction of the genome? Thousands? Millions? Billions? What the heck does it mean?

If these “much” statements of ID proponents have a definite meaning, they are factually false. If they have no definite meaning, they are not predictions and simply misleading.Mr. Luskin: Do not say “much” ever again. Tell your readers: what fraction of nucleotides in human DNA will be functional, meaning biochemically constrained as to sequence?

Category #2 is to claim that entire classes of junk DNA are all functional, every last nucleotide of every last one, if an example can be found in which a small fraction of an instance of that type of junk DNA is functional.

Casey Luskin: “Darwinists have commonly made this mistake with many types of "junk" DNA, now known to have function.”This is false: in fact there are no types of junk DNA now known to have a function; if by “have a function” we mean that most or all of their nucleotides are biochemically constrained.

Here is an example of the trick they pull. There are about 20,000 pseudogenes in the human genome, and a typical pseudogene may be 1,000 nucleotides. If 10 of those nucleotides (0.1% of one pseudogene out of 20,000) have been co-opted as, say, a regulatory element, then ID proponents like Jonathan Wells and Luskin assert that that whole pseudogene is now functional (because 0.1% of its nucleotides are constrained) and by extension, that that “type” of junk DNA is now proven to be “functional”, implying that all 20,000 pseudogenes are functional.

In this way, ID proponents like Jonathan Wells and Luskin mislead their readers into thinking that 20-30 million nucleotides are now “functional”, because of the discovery of a few dozen functional nucleotides.

They then repeat the trick for other classes of junk DNA, like defective transposons, Alus, etc. Presto! The whole genome is functional!

Continuing with my post to Luskin's "junk DNA" claim in the list of Top 10 problems with evolution [part 3]:

Category #3 is for ID proponents to make quantitative statements that are simply false. For example, in the OP above, Mr. Luskin linked to this ENV posting which supposedly has evidence about false predictions of “Neo-Darwinism.”

Here we find a rare quantitative (but obviously false) statement:

“But the [tiling array] study goes further, indicating for the first time that the vast majority of the 3 billion 'letters' of the human genetic code are busily toiling at an array of previously invisible tasks.”

(Uh, for the first, and last, time.) At least that’s quantitative, but what’s wrong with it? It’s from a 2007 newspaper article, not a scientific publication, five years out of date and not correct when it was published. The claims that most of the genome is functional are all based on experiments using tiling arrays that allegedly showed almost all the genome was transcribed into RNA, though most of it at an extremely low level.

However, the idea that ‘transcribed’ means ‘functional’ is a big assumption (the article uses the phrase “toiling away”), and at any rate, more recent research contradicts the 2007 claim. In 2010 research using a more accurate method, RNA-seq, showed that the tiling array data was unreliable and overestimated transcription, possibly due to cross-hybridization (in addition the RNA transcription apparatus is not perfectly specific and may make mistakes on rare occasions, still detectable by tiling arrays.) What’s worse, much of the transcribed regions are not evolutionarily conserved and/or are repetitive. Very hard to believe all that could be functional.

Larry Moran predicted results like this before the van Bakel study was published. No ID proponent predicted this. Another falsified prediction of ID.

So what fraction of nucleotides in the human genome are known to be functional?Larry Moran summarizes what we really know about junk DNA. As of May, 2011, we know at least 8.7% of the human genome is essential or functional. As for junk, it is between 65 to 91.3%.

Genes make up about 2% of the human genome. Currently we believe regulatory elements are smaller than genes. But let’s we go hog-wild, and let’s imagine that regulatory elements were 10 times larger than genes. Even in Casey’s dreams, well over 70% of the genome is still junk.

The "Intelligent design" notion (I will not call it a theory) posits the existance of an intelligent designer, based on the intelligence they imagine behind the order in the physical world.

I ask them:

Does a TV have an intelligent design? They answer yes.

In fact it doesn't. There are thousands of individual innovations, patents, and improvements behind a common contemporary TV. Not one designer, but thousands.

Each such innovation provides a metaphor for the many individual adaptations that have rendered today's species.

Just as market and technical pressures and the imperative to survive force certain design changes (improve or fail), others provide an advantage over competing species (improve and succeed) or models of televisions.

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.